Into The Dark
by anonymous1222
Summary: A virus has spread causing Pokemon to fall into a feral state, but is the virus really an act of nature or is someone working from the shadows? Ash and the gang, along with a young man with a tragic past have to put an end to the virus before its too late


Into The Dark

The young man's hands shot to his right eye as he screamed out in indescribable pain. He fell to his knees, desperately trying to block out the pain that shot through his face, when he heard his sister scream. He opened his good eye and watched in horror as the Gengar slashed down upon his older sister.

Rage boiled through the young man as his sister's body went limp. "No," he screamed as he charged sluggishly toward the dark purple Pokemon, but with ethereal grace and a grin that seemed to wide for its face, it jumped out of the way and the young man lost his balance and fell beside his sister's lifeless body. The malicious Pokemon stood over him, cackling, and raised its arm, ready to slash him again, when the boy reached for the black and yellow pokeball at his sister's belt and threw it at the shadow.

The ball made contact with the Pokemon, vaporizing it instantly in a swarm of red light, before snapping shut, containing it within the capsule. The young man lay motionless in the wreckage of his home, surrounded by the lifeless bodies of his parents and Pokemon, as the ball rocked back and forth several times before finally resting still. And with the battle over, the exhausted young man closed his eyes and fell into a deep sleep.

A1222

Two Years Later

Ash Ketchum walked past the now-defunct daycare center of Route 5 and stopped to take a deep breath. "Well, Pikachu," he said as the mouse-Pokemon crawled up the trainer's body and onto his shoulder, "It's been a few years, but we're finally back in good old Kanto." A wide grin appeared on his face as focused his gaze on the Gym in the middle of town. It's bright lights and elaborate ocean-themed design sticking out like a sore thumb in the dark night made him that much more eager to not waste any more time in reuniting with his friends.

Ash turned to Pikachu and, unable to contain his excitement any longer, shouted "Let's go," and broke into a sprint, forcing Pikachu to jump down from his perch and run alongside him.

He ran down the quiet streets of Cerulean City, using the lights from the gym as his guide as he darted between the scattered stores and houses of the city. When he reached the large double doors of the gym he stopped and looked up at the magnificent building.

"So many memories," he said to himself with a smile as he reflected on his first Pokemon battle with Misty almost eight years ago. He then closed his eyes and briefly wondered how Butterfree and Pidgeot had been since he released them.

Opening his eyes, Ash took one last look up at the gym before opening the door and heading inside.

Ash was surprised to find that all the main lights in the entrance had been turned off. The only light available came from the faint glow provided by the many Chinchou and Lanturn in the aquarium that served as interior walls for the gym.

'_Where is everyone?' _Ash thought to himself as he made his way down the hallway toward the swimming pool, '_Misty told me they'd be here, but it doesn't look like anybody's shown up.' _

Ash looked down at Pikachu and asked, "You don't think something bad has happened, do you?"

"Pika…" Pikachu said, sounding slightly worried.

"Nah," Ash exclaimed as he and his partner reached the door to the pool, "I'll bet they're all just waiting inside to," he opened the door and stared, dumbfounded, at the scene, "welcome…us….back…."

Unlike the entrance and the hallway, all of the lights in the pool area were still on, and on a beach chair that sat on a small island in the middle of the pool was a redheaded girl curled up and fast asleep.

"Well," Ash whishpered as he turned to Pikachu, barely able to contain his joy at seeing his old friend, "at least me know Misty's okay."

"C'mon," Ash said as he reached down and picked Pikachu up, placing him on his shoulder as he walked up to the thin stretch of land at the side of the pool that led to the little island and carefully made his way toward his sleeping friend. When he reached the island, Ash turned to Pikachu and held a finger to his lips and whispered, "Shhh," as he slowly walked up to the beach chair.

Ash knelt down beside his friend, leaned in close to her ear, and whispered, "Misty, wake up."

The girl moaned a bit and shifted in the chair, but remained fast asleep.

Speaking a littler louder now, Ash repeated, "Misty, wake up."

Again, Misty shifted around, but still remained asleep, so Ash decided that he would need a change of tactics.

Ash leaned in once more and whispered, "It's great seeing you again," and then he kissed her gently on the forehead, and Misty slowly opened her eyes. "Good morning," Ash said to his friend who stared up at him blankly.

"Ash?" she asked softly, as if wondering if this was just some dream.

"Yup, I'm finally back," Ash smiled as his friend slowly sat up in the chair. Her eyes barely opened, Misty smiled back at Ash and she reached forward to put her hand on Ash's cheek. "It's good to be—"

–-Slap—

Misty smacked Ash across the face as hard as she could, cutting him off. Pikachu just barely managed to jump off of Ash's shoulder and onto the island as the trainer toppled backward into the pool from the force of the blow. "You're late," Misty stood up from the chair and shouted at her friend wading on the surface of the water, "You were supposed to be here hours ago, what happened?"

Ash chuckled, "I'm sorry. The ferry to Vermillion was delayed. Where is everyone?"

"Misty, are you okay," Brock said as he charged into the pool from the door at the back, "I heard shouting."  
>"Hey, Brock," Ash waved from the water toward his friend and started swimming to the edge of the pool.<p>

"Ash," Brock exclaimed as he ran to the pool and helped Ash out of the water. "What took you so long?"

"Just got delayed a little. How have you been?"

"I've been good. Things have been a little hectic with some of the Pokemon, but nothing I can't handle." Brock patted Ash on the back, sending drops of water flying everywhere, "Oak will be excited to hear that you finally arrived."

"Is he too?"

"Yeah, we all slept in the guest quarters here at the gym….well," Brock looked over at Misty from the corner of his eye, "all except Misty here who insisted she wait for you."

"Shut up, Brock," Misty said, her face growing slightly red as she turned her head away from her friends, "I just…didn't want Ash coming back to an empty gym and thinking we'd gotten attacked or something."

"Thanks," Ash placed a hand on Misty's, causing the redhead to blush even more, "I'm glad that you did."

She couldn't help but smile back at her friend and give him a huge hug despite the fact that he was soaking wet.

"Why don't I go get the Professor?" Brock suggested.

"No," Ash stopped him before he could turn to leave, "let him sleep. I'll catch up with him tomorrow when everyone's refreshed." Brock was shocked to hear something so mature coming from his friend, but nonetheless accepted his proposal.

"Well," the trainer said, "in that case, I think I'll head back to bed too."

With a wave, Brock turned around and headed for the door to the guest quarters.

Once Brock made it through the door, Ash turned to Misty, "Why don't you go get some sleep too? I don't want you staying up for my sake."

"No, I'm okay," she said, "Come on," she grabbed his hand and led him to the pool entrance, "let's find somewhere to talk."

A1222

Misty dipped her feet in the water at Cerulean Cape as Ash sat down cross-legged next to her. He stared up at the stars, wondering just what Misty wanted to talk about that couldn't wait until everyone else was awake. He watched as the beacon from Bill's Lighthouse spun circles in the sky when Misty finally spoke up. "Ash," she started, "why were you gone for so long?"

"Hmmm?" Ash was unsure of what she meant, they had gone over this when he first set out, "I had heard reports of new Pokemon findings in America, so I wanted to check it out. But the voyage is a lot longer than travelling to somewhere like Johto. So of course I was going to be gone for quite some time."

"But four years? How could it have taken you four years?" Misty pulled her knees in close to her chest, "I was really worried out you. You never contacted any of us."

"Things were different out there. The American regions aren't anything like the ones here in Japan. Out here it's like living in the wilderness everywhere you go. Even the major cities felt like the frontier."

"But it was FOUR YEARS," Misty got to her feet and shouted at Ash, "for four years I haven't seen you, heard from you…and then when you finally show up you expect me to ignore the fact that my best friend, someone I would risk my life for, seemed to forget about me all this time?"

"Misty—"

"Every day I waited….I waited for something, some sign that you were coming back. But the only reason I had to not think you were dead was the fact that every few weeks Oak would call to tell me you transferred some new Pokemon."  
>"MISTY," Ash said forcefully as he got to his feet, "I am sorry. I know I should have contacted you. But after what you told me before I left, I wasn't sure of what to say."<p>

"What about now?" Misty said, calming down considerably as she took a step closer to Ash. "If I were to tell you the same thing again, what would you say?"

Ash took a step toward Misty, closing the gap between them so that they were only a few inches apart, "Yes." Ash put his hand on the back of Misty's neck and leaned in to kiss her. He found no resistance as Misty wrapped her arms around Ash and pulled him in tighter.

After what seemed like an eternity, the two broke the kiss and Misty buried her head in Ash's chest as Ash put his arms around her back and held her close. "Ash," Misty said softly, "you really have grown up." Until now she had always been quite a bit taller than Ash, but she found the recent shift to be quite comforting.

Separating slightly, Misty looked up into Ash's eyes and whispered, "Happy Birthday," before leaning in for another kiss…

A1222

Ash, Misty, Brock, and Professor Oak sat at a small table set up by the pool early that morning to discuss Ash's journey. "Here you go," Ash said as he dug a pokedex out of his backpack and handed it to the professor, "You'd be amazed at some of the Pokemon I saw out there."

"Yes," Professor Oak said as he opened the pokedex and started reading through the files, "I noticed with some of the Pokemon that you sent back to me that the American zones seem to be the home of Pokemon that rely much more on physical strength than those found around here."

"So what does that mean?" Brock asked, "Do they not focus much on status manipulation?"  
>"Not so much," Ash said as he thought back to all the Pokemon he encountered, "occasionally you'd run into a Pokemon who knew something like hypnosis or poison powder, but it seemed like most of the Pokemon out there focused on hitting hard and fast rather than slowly working at the opponent."<p>

"That's right up your alley then, isn't it, Ash?" Misty smirked.

"Oh very funny." Ash said, "But I have to tell you, it's completely different. Being chased by a horde of Rhyhorn is nothing compared to some of the stuff I had to deal with. On my first day I got attacked by a family of Magnataur, but thankfully Pikachu was there to save my sorry ass."

"Magnataur, what's that?" Misty asked.

"Hey, Professor, do you think you could pull up its file real quick."

"Sure thing, Ash," Oak hit a button on the pokedex and laid it down on the table so that the screen was facing Misty and Brock.

A picture of a Pokemon that resembled a one-tailed Tauros that's been shortened, beefed up, and doused in flames popped up, "Magnataur, the Fire-Bull Pokemon," the pokedex started in its monotone computed voice, "the flames that cover its body only reach temperatures hotter than 30 degrees Celsius when it becomes enraged. These Pokemon are known for their temper and trainers are advised to practice extreme caution while attempting to confront one." Professor Oak picked up the pokedex and resumed his reading.

Brock was the first one to speak up, "It looks a lot like Tauros."

"Yeah," Ash said, "I was surprised at the similarity too. But I found that a lot of Pokemon over in America resembled Pokemon found over here. I think they may actually be related somehow."

"Did you manage to catch one?" Misty asked.

"Yeah," Ash said proudly, "It was difficult, but I managed to catch one that Pikachu hit with a thunderbolt."

"Oh, that reminds me," Oak said. He put the pokedex down and pulled up his satchel. "I have the Pokemon you requested, Ash," he handed the bag to Ash who happily accepted it and started clipping the Pokeballs he found inside to his belt.

"Which Pokemon did you take out?" Misty asked, hoping to see more of the Pokemon that Ash encountered in the hopes that he brought back a few water Pokemon.

"Oh," Ash said as he clipped the last Pokeball to his belt, "Just some of the gang that I haven't seen in a while. I figure that, since I'm back at Kanto, I should take them out for old time's sake."

"Well," Professor Oak said as he slipped the Pokedex into his satchel before placing the bag by his feet, "now that we are all reacquainted, it's time I tell you why I called you all here." Oak leaned forward in his seat and stared at the trio sternly, "I have been doing some research with Blaine down in Cinnabar after hearing reports of Pokemon becoming increasingly aggressive throughout the region. At first we believed it to simply be the Pokemon reacting to humans expanding their cities, but as our researched continued we found that the answer was not so simple, nor was it so fortunate."

Professor Oak paused and the three trainers leaned in, eagerly waiting to hear just what it was that his research had unveiled. "I'm afraid," he continued, "That the sudden increase in aggression is not merely a reaction to humans. It has been occurring far too rapidly and much to large a scale for that to be the case. What our research has shown is that this is the work of a virus."

Brock and Misty gasped at what they heard, but Ash remained calm, "Well, aren't there ways to counter that? Can't you make some type of medicine to prevent this virus from spreading?"  
>"I'm afraid that's easier said than done, Ash." Oak said, "If this virus were found in one isolated area, then yes, that course of action would be easy to follow. But by the time we knew what was happening, it had already spread throughout Kanto."<p>

"So this is why there have been so many reports recently about Pokemon attacks near the larger cities," Brock said, "Of course there's always been an inherent danger in being a Pokemon trainer, but normally Pokemon that live near human settlements tend to become docile fairly quickly. Yet the amount of cases of people getting attacked near settlements has skyrocketed in the past few weeks."

"Yes," Professor Oak said, "it would explain such occurrences. But let's not forget Pokemon that live far away from repetitive human contact. There have been far too many reports of trainers going missing as they travel from city to city for it to be mere coincidence. If those numbers mean anything, they show that the virus doesn't simply make Pokemon aggressive."  
>"What do you mean, Professor?" Misty asked.<p>

"Misty, do I have your permission to bring out a Pokemon?"

"Of course."  
>"Thank you," Professor Oak stood up and pulled a Pokeball out from the breast pocket of his lab coat. He expanded it to full size and threw it, releasing a Parasect in a flash of red light.<p>

The parasect looked at its surroundings before locking onto Ash, "Professor," the trainer said, not paying much attention to the Pokemon, "I don't see your point. The way you were describing it I would have thought—" before he could finish the sentence the Parasect charged forward and leapt through the air, claws out, aiming for Ash, but was stopped when Oak returned it to the Pokeball. "What the hell!" Ash screamed.

"Parasect," Oak started, "as I'm sure you all know, are fairly peaceful Pokemon, normally only attacking when directly threatened. However, this one had no problem with striking first, even without provocation."

"Professor," Misty said, "what about Pokemon that aren't in the wild?"  
>"They are at risk too. But from what I have gathered, their constant interaction with humans seems to diminish the effect that the virus has on their system."<br>"Professor, what does this mean?" Ash asked, slightly shaken by what had just happened, "If this virus just makes Pokemon more aggressive, that can be dealt with. But the way you're talking about it makes it seem like there's more to it."  
>"At this point," Oak turned his back to the group and pocketed the pokeball, "a simple aggression augmentation would be a best case scenario. But after running through all the tests, Blain and I have come to realize that this virus likely does something much worse." The professor turned back to the trainers and said, in a tone far more stern than any of them had ever heard from him before, "This virus doesn't make Pokemon aggressive. It makes them downright feral." The three trainers stared at the professor, horrified at what he had just said.<p>

"Professor," Ash started, "what can we do to stop this?"

"At this point I'm not sure. We can't simply divulge this information to the masses, but Blain and I both feel that having some strong trainers at the ready is a good precaution."  
>"Why's that?" Ash asked for the three of them.<p>

"Because there is strong evidence that shows that this virus is not some act of nature. And all of our clues lead to one man, Ash. Someone who you have had quite some experience with in the past. Someone who, as far as we know, should be dead." Ash's eyes widened as the realization about who exactly Professor Oak was talking about hit him. "Ash, Giovanni is back."

A1222

"Dani…" the voice whispered to the young man as he pulled a pillow over his head to try and block out the voice, "Dani…" it repeated, sounding as if the pillow had no effect, "You can't hide from me forever."

"Get out of my head," the young man shot up in his bed at the Gym, holding the right side of his face. Drenched with sweat and panting like a dog, he got out of bed and walked to the bathroom.

He turned on the faucet and splashed his face with cold water when the voice came again, "Dani…" he quickly turned around, half-expecting to see the source of the voice despite knowing that to be impossible.

Shaking, he turned back around and pressed his forehead against the glass of the mirror. "Why….why can't you just leave me alone?" Laughter echoed in his head as the presence and the voice finally began to fade away. Finally able to calm down he leaned away from the mirror and looked at his reflection.

His pale skin and already greying hair were both a result of the torment he received from the voice. It gave him the appearance of someone who was very sick—two years of torment from the Pokemon he had kept sealed in its pokeball for two years had clearly taken its toll on Dani Shade. But none of his features were as distinctive, or shocking, as the large purple scar that ran from his hairline, straight down through his right eye all the way to his upper lip. His right eye, now a ghostly white, had lost all its vision in the attack two years ago. And as Dani wrapped bandages around the right side of his face, he couldn't help but tremble as he thought back to the night when one Gengar killed his sister and all of their Pokemon.

Having finished wrapping his face, he walked back to his bed and pulled out a box from beneath. He slowly opened the lid and stared at the yellow and black pokeball within. He reached for it with a trembling hand and as he got closer and closer he could feel the presence of the malicious Pokemon within, but he shut his eyes and quickly snatched the Pokeball, securing it to his belt.

As he made his way out of his room, he could hear the faint sound of laughter echoing in the back of his head.

A1222

There's the first chapter, It's been a while since I've posted any fanfic, but I hope you enjoyed. Please review.


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